rs1522889

Variant names:

• chrX-121390334-C-A
• rs1522889

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.428 in 110,717 control chromosomes in the GnomAD database, including 7,785 homozygotes. There are 13,567 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.43 (7785 hom., 13567 hem., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.186

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.491 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.428 AC: 47321 AN: 110663 Hom.: 7788 Cov.: 22 AF XY: 0.411 AC XY: 13544 AN XY: 32949

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.353

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.567

Gnomad EAS AF: 0.0133

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.414

Gnomad MID AF: 0.543

Gnomad NFE AF: 0.496

Gnomad OTH AF: 0.451

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.428 AC: 47337 AN: 110717 Hom.: 7785 Cov.: 22 AF XY: 0.411 AC XY: 13567 AN XY: 33013

Gnomad4 AFR AF: 0.386

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.567

Gnomad4 EAS AF: 0.0133

Gnomad4 SAS AF: 0.362

Gnomad4 FIN AF: 0.414

Gnomad4 NFE AF: 0.497

Gnomad4 OTH AF: 0.450

Alfa AF: 0.467 Hom.: 11235

Bravo AF: 0.414

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.66

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1522889; hg19: chrX-120524188;